spaCR

spaCR links pooled CRISPR-Cas9 perturbations to single-cell spatial phenotypes in high-content microscopy images. It segments cells, nuclei, pathogens and organelles with Cellpose, measures morphology, intensity, texture and colocalization features into a SQLite project, trains image and measurement classifiers, maps sequencing reads to wells and gRNAs, and estimates per-guide and per-gene effects by regression.